5XUZ | pdb_00005xuz

Crystal structure of Lachnospiraceae bacterium ND2006 Cpf1 in complex with crRNA and target DNA (CCCA PAM)

• PDB DOI: https://doi.org/10.2210/pdb5XUZ/pdb
• NAKB: 5XUZ

• Classification: HYDROLASE/RNA/DNA
• Organism(s): Lachnospiraceae bacterium ND2006, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-06-26 Released: 2017-08-09 
• Deposition Author(s): Yamano, T., Nishimasu, H., Ishitani, R., Nureki, O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.229 (Depositor), 0.232 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: experimental

Literature

Structural Basis for the Canonical and Non-canonical PAM Recognition by CRISPR-Cpf1.

Yamano, T., Zetsche, B., Ishitani, R., Zhang, F., Nishimasu, H., Nureki, O.

(2017) Mol Cell 67: 633-645.e3

• PubMed: 28781234 
• DOI: https://doi.org/10.1016/j.molcel.2017.06.035
• Primary Citation Related Structures: 
  5XUS, 5XUT, 5XUU, 5XUZ


• PubMed Abstract: 
  

  The RNA-guided Cpf1 (also known as Cas12a) nuclease associates with a CRISPR RNA (crRNA) and cleaves the double-stranded DNA target complementary to the crRNA guide. The two Cpf1 orthologs from Acidaminococcus sp. (AsCpf1) and Lachnospiraceae bacterium (LbCpf1) have been harnessed for eukaryotic genome editing. Cpf1 requires a specific nucleotide sequence, called a protospacer adjacent motif (PAM), for target recognition. Besides the canonical TTTV PAM, Cpf1 recognizes suboptimal C-containing PAMs. Here, we report four crystal structures of LbCpf1 in complex with the crRNA and its target DNA containing either TTTA, TCTA, TCCA, or CCCA as the PAM. These structures revealed that, depending on the PAM sequences, LbCpf1 undergoes conformational changes to form altered interactions with the PAM-containing DNA duplexes, thereby achieving the relaxed PAM recognition. Collectively, the present structures advance our mechanistic understanding of the PAM-dependent, crRNA-guided DNA cleavage by the Cpf1 family nucleases.

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Organizational Affiliation: 
• Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.
Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan. Electronic address: [e-mail].
Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 337.58 kDa 
• Atom Count: 23,419 
• Modeled Residue Count: 2,580 
• Deposited Residue Count: 2,618 
• Unique protein chains: 1
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LbCpf1	A, E	1,231	Lachnospiraceae bacterium ND2006	Mutation(s): 0
UniProt
Find proteins for A0ACD6BAZ6 (Lachnospiraceae bacterium ND2006) Explore A0ACD6BAZ6  Go to UniProtKB:  A0ACD6BAZ6

Entity ID: 2
Molecule	Chains	Length	Organism	Image
crRNA	B, F	40	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (29-MER)	C, G	29	synthetic construct

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*GP*TP*CP*CP*CP*CP*CP*A)-3')	D, H	9	synthetic construct

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	J [auth A], L [auth B], O [auth E], Q [auth F]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG	I [auth A], N [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	K [auth B], M [auth C], P [auth F]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.229 (Depositor), 0.232 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.946	α = 90
b = 103.54	β = 90
c = 342.683	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-08-09 
Deposition Author(s): Yamano, T., Nishimasu, H., Ishitani, R., Nureki, O.

Revision History  

• Version 1.0: 2017-08-09
  Type: Initial release
  
• Version 1.1: 2017-12-06
  Changes: Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description